Wikiomics:Crystallography toolbox

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==Data integration==
==Data integration==
-
* denzo (from HKL [http://www.hkl-xray.com/])  
+
* [http://www.hkl-xray.com/ denzo]) (from HKL)
-
* mosflm (from ccp4 [http://www.ccp4.ac.uk/])  
+
* [http://www.ccp4.ac.uk/ mosflm] (from ccp4)  
-
* d*TREK [http://www.csb.yale.edu/userguides/datamanip/dtrek/dtrek_descrip.html]
+
* [http://www.csb.yale.edu/userguides/datamanip/dtrek/dtrek_descrip.html d*TREK ]
-
* XDS [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/]
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* [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/ XDS]
===Scaling===
===Scaling===
* scalepack (from HKL)  
* scalepack (from HKL)  
-
* scala (from ccp4)  
+
* [http://www.ccp4.ac.uk/ scala] (from ccp4)  
* xprep (from xprep/Bruker)  
* xprep (from xprep/Bruker)  
-
* XSCALE [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html]
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* [http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html XSCALE]
==Phasing==
==Phasing==
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* AMoRe (from ccp4)  
* AMoRe (from ccp4)  
* Phaser (from ccp4)  
* Phaser (from ccp4)  
-
* EPMR [http://www.msg.ucsf.edu/local/programs/epmr/epmr.html]
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* [http://www.msg.ucsf.edu/local/programs/epmr/epmr.html EPMR]
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* Queen of Spades [http://www.mbg.duth.gr/~glykos/Qs.html]
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* [http://www.mbg.duth.gr/~glykos/Qs.html Queen of Spades]
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* COMPANG [http://journals.iucr.org/j/issues/2002/05/00/vi0166/vi0166bdy.html]
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* [http://journals.iucr.org/j/issues/2002/05/00/vi0166/vi0166bdy.html COMPANG]
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* BRUTEPTF (phased molecular replacement, http://russel.bioc.aecom.yu.edu/server/NYSGRC.html)  
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* [http://russel.bioc.aecom.yu.edu/server/NYSGRC.html BRUTEPTF ] (phased molecular replacement)
===Heavy atom methods===
===Heavy atom methods===
====Patterson methods====  
====Patterson methods====  
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* SOLVE [http://www.solve.lanl.gov/]
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* [http://www.solve.lanl.gov/ SOLVE]
* fft (from ccp4)  
* fft (from ccp4)  
-
* xHercules (from xtalview [http://www.sdsc.edu/CCMS/Packages/XTALVIEW/xtalview.html])  
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* xHercules (from [http://www.sdsc.edu/CCMS/Packages/XTALVIEW/xtalview.html xtalview])  
====Direct and dual-space methods====  
====Direct and dual-space methods====  
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* SHELX-D [from shelex http://shelx.uni-ac.gwdg.de/SHELX/]
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* SHELX-D from  [http://shelx.uni-ac.gwdg.de/SHELX/ shelex ]
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* Shake and Bake (SnB) [http://www.hwi.buffalo.edu/SnB/]
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* [http://www.hwi.buffalo.edu/SnB/ Shake and Bake (SnB)]
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* Rantan (from ccp4)  
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* Rantan (from ccp4)
====Ab initio methods====
====Ab initio methods====
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===Phase refinement===
===Phase refinement===
-
* SHARP/autoSHARP (SHARP suite [http://www.globalphasing.com/sharp/])
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* [http://www.globalphasing.com/sharp/ SHARP/autoSHARP] SHARP suite
* Mlphare, Vecref (from ccp4)  
* Mlphare, Vecref (from ccp4)  
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* Resolve http://www.solve.lanl.gov/
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* [http://www.solve.lanl.gov/ Resolve]
* SHELX-E  
* SHELX-E  
* DM (from ccp4)  
* DM (from ccp4)  
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**Fffear, ffjoin (from ccp4)  
**Fffear, ffjoin (from ccp4)  
* Interactive model building  
* Interactive model building  
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**O (from Uppsala Software Factory) [http://xray.bmc.uu.se/~alwyn/]
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**[http://xray.bmc.uu.se/~alwyn/ O ](from Uppsala Software Factory)
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** coot [http://www.ysbl.york.ac.uk/~emsley/coot/
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**[http://www.ysbl.york.ac.uk/~emsley/coot/ coot]
**Quanta [http://www.accelrys.com/products/quanta/]
**Quanta [http://www.accelrys.com/products/quanta/]
**Xtalview  
**Xtalview  
-
**Turbo Frodo [http://www.afmb.univ-mrs.fr/-TURBO-]
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**[http://www.afmb.univ-mrs.fr/-TURBO- Turbo Frodo]
==Model refinement==
==Model refinement==
-
* CNS [http://cns.csb.yale.edu/]
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* [http://cns.csb.yale.edu/ CNS]
* refmac (from ccp4)  
* refmac (from ccp4)  
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* TNT [http://www.uoxray.uoregon.edu/tnt/]
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* [http://www.uoxray.uoregon.edu/tnt/ TNT]
   
   
==Structure validation==
==Structure validation==
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* Procheck [http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html]
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* Procheck [http://www.biochem.ucl.ac.uk/~roman/procheck/procheck.html Procheck]
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* WhatIf [http://www.sander.ebi.ac.uk/whatif/]
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* [http://www.sander.ebi.ac.uk/whatif/ WhatIf]
==Utilities==
==Utilities==
* Uppsala Software Factory (USF) [http://alpha2.bmc.uu.se/usf/]
* Uppsala Software Factory (USF) [http://alpha2.bmc.uu.se/usf/]
-
* ccp4
+
* [http://www.ccp4.ac.uk/ ccp4]
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[[Category:Protocol]] [[Category:In silico]] [[Category:Data analysis]]

Current revision

Crystallography toolbox

Contents

Data processing

Data integration

Scaling

  • scalepack (from HKL)
  • scala (from ccp4)
  • xprep (from xprep/Bruker)
  • XSCALE

Phasing

Molecular replacement

Heavy atom methods

Patterson methods

Direct and dual-space methods

Ab initio methods

  • Acorn (from ccp4)
  • Oasis (from ccp4)

Phase refinement

  • SHARP/autoSHARP SHARP suite
  • Mlphare, Vecref (from ccp4)
  • Resolve
  • SHELX-E
  • DM (from ccp4)
  • Dmmulti (from ccp4)
  • SOLOMON (from ccp4)

Model building

Model refinement

Structure validation

Utilities

  • Uppsala Software Factory (USF) [2]
  • ccp4


Credits

Template:Credits

  • Tina Bakolitsa wrote this list
  • Darek Kedra translated it into wiki and added links


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